In this study, phylogenetic and morphological studies of Salmo trutta fario isolate Persicus with partial and complete mitochondrial sequencing was carried out. The full length and partial sequencing (NADH 1 gene) were sequenced and deposited in GenBank accession numbers LC137015, LC137894, LC154931, LC1549281, and LC011387.1. Almost all meristic traits values were the same between Salmo trutta fario caught from the four regions Cheshmeh Kile, Jaj Roud, Ghasem Abad and Siahkal Roud. On the other hand, studies of molecular phylogenetic-based Maximum Parsimony between Salmo trutta fario isolate Persicus and another 50 nucleotide sequences of Salmonid species showed low variation between Salmo trutta fario (LC137015), Salmo trutta caspius (LC011387.1) and Salmo Salar (different accession numbers). Moreover, Maximum Composite Likelihood Estimate conducted was conducted using MEGA software version 7.0. According to that, rates of different transitional and transversional changes are shown. The resulting nucleotide frequencies are 29.76% (A), 26.34% (T/U), 24.24% (C) and 19.66% (G). The transition/transversion rate ratios are k1= 23.652 (purines) and k2 = 0.053 (pyrimidines). The analysis involved five nucleotide sequences. According to the lengths of branches, salmo trutta fario – Jaj Roud 1 (LC154929), salmo trutta fario-Jaj Roud 2 (LC154931.1), salmo trutta fario-Siahkal Roud (LC1549281), salmo trutta fario-Cheshmeh Kileh (LC137015), and salmo trutta fario-Ghasem Abad (LC137894) variety were different, respectively. Comparison of partial mitochondrial sequence in Salmo trutta fario for the four regions cited above showed that approximately 99% homology existed between them. In conclusion, the mitochondrial genome homology of Salmo trutta fario and other salmonids were high.